[BioC] Possible to set alternative colnames on read.flowSet (flowCore)

[Florian Hahne]

Yes there is.
 From the documentation of read.flowSet:
name.keyword: An optional character vector that specifies which FCS
          keyword to use as the sample names. If this is not set, the
          GUID of the FCS file is used for sampleNames, and if that is
          not present (or not unique), then the file names are used.

Florian


Aric Gregson wrote:
> Hello,
>
> I would like to be able to set the colnames of a flowSet to the user
> defined labels at the time of reading in the flowSet with read.flowSet.
> I'm not sure how to go about doing this. From the output of keyword(fs
> [[1]]) the colnames are taken from the $PXN keyword, but I would like
> to specify it use $PXS keyword instead. 
>
> $`$P16N`   --------------> used by read.flowSet as colnames
> [1] "Indo-1 (Violet)-A"
>
> $`$P16S`   --------------> would like to use instead
> [1] "BlueUV-Live"
>
> Is there a way to specify this with read.flowSet? Thanks for any
> pointers. 
>
> Aric
>   


-- 
Florian Hahne, PhD
Computational Biology Program
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-3148
fhahne at fhcrc.org